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- PDB-5oqh: Crystal Structure of a disulfide trapped single chain trimer comp... -

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Basic information

Entry
Database: PDB / ID: 5oqh
TitleCrystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C K66A mutant, beta-2microglobulin, and ovalbumin-derived peptide
ComponentsBeta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / Diagnosis / Epitopes / Major Histocompatibility Complex / Mice / Models / Molecular / Molecular Conformation / Peptides / Receptors / Antigen / T-Cell / T-Lymphocytes / Vaccines
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMikolajek, H. / Werner, J.M. / Beton, M.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L010402/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The partial dissociation of MHC class I-bound peptides exposes their N terminus to trimming by endoplasmic reticulum aminopeptidase 1.
Authors: Papakyriakou, A. / Reeves, E. / Beton, M. / Mikolajek, H. / Douglas, L. / Cooper, G. / Elliott, T. / Werner, J.M. / James, E.
History
DepositionAug 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)96,2472
Polymers96,2472
Non-polymers00
Water8,323462
1
A: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,1241
Polymers48,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain


Theoretical massNumber of molelcules
Total (without water)48,1241
Polymers48,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.460, 89.320, 89.400
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-2-microglobulin,H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 48123.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887, UniProt: P01901
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Am sulphate, 25 % PEG 8K, 0.1M Na cacodylate pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.05→39.36 Å / Num. obs: 59951 / % possible obs: 98.1 % / Redundancy: 3.8 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRI

2qri


Resolution: 2.05→39.36 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.13
RfactorNum. reflection% reflection
Rfree0.2419 3030 5.06 %
Rwork0.2049 --
obs0.2069 59938 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6292 0 0 462 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026474
X-RAY DIFFRACTIONf_angle_d0.5418792
X-RAY DIFFRACTIONf_dihedral_angle_d3.8973838
X-RAY DIFFRACTIONf_chiral_restr0.041908
X-RAY DIFFRACTIONf_plane_restr0.0031142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.0820.35911310.27232581X-RAY DIFFRACTION97
2.082-2.11620.37671300.27292507X-RAY DIFFRACTION97
2.1162-2.15270.32711570.25952539X-RAY DIFFRACTION97
2.1527-2.19180.30571490.2572572X-RAY DIFFRACTION97
2.1918-2.23390.28871170.24662567X-RAY DIFFRACTION97
2.2339-2.27950.31821250.2372556X-RAY DIFFRACTION97
2.2795-2.32910.2431130.24392572X-RAY DIFFRACTION98
2.3291-2.38330.29951380.24022596X-RAY DIFFRACTION98
2.3833-2.44290.31841410.23382562X-RAY DIFFRACTION98
2.4429-2.50890.2641160.22912579X-RAY DIFFRACTION98
2.5089-2.58270.25811310.2342610X-RAY DIFFRACTION98
2.5827-2.66610.31011540.23492575X-RAY DIFFRACTION98
2.6661-2.76130.27291340.23792604X-RAY DIFFRACTION99
2.7613-2.87190.27911620.22642571X-RAY DIFFRACTION98
2.8719-3.00250.24361410.21232594X-RAY DIFFRACTION98
3.0025-3.16070.20851350.21462583X-RAY DIFFRACTION98
3.1607-3.35870.23071550.19862583X-RAY DIFFRACTION99
3.3587-3.61780.23151340.18532632X-RAY DIFFRACTION99
3.6178-3.98160.22181360.17542605X-RAY DIFFRACTION99
3.9816-4.5570.20191490.15892612X-RAY DIFFRACTION99
4.557-5.73850.19131420.16932645X-RAY DIFFRACTION99
5.7385-39.37010.19871400.19772663X-RAY DIFFRACTION98

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